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Polito JT, Lange I, Barton KE, Srividya N, Lange BM. Characterization of a Unique Pair of Ferredoxin and Ferredoxin NADP + Reductase Isoforms That Operates in Non-Photosynthetic Glandular Trichomes. Plants (Basel) 2024; 13:409. [PMID: 38337942 PMCID: PMC10857128 DOI: 10.3390/plants13030409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024]
Abstract
Our recent investigations indicated that isoforms of ferredoxin (Fd) and ferredoxin NADP+ reductase (FNR) play essential roles for the reductive steps of the 2C-methyl-D-erythritol 4-phosphate (MEP) pathway of terpenoid biosynthesis in peppermint glandular trichomes (GTs). Based on an analysis of several transcriptome data sets, we demonstrated the presence of transcripts for a leaf-type FNR (L-FNR), a leaf-type Fd (Fd I), a root-type FNR (R-FNR), and two root-type Fds (Fd II and Fd III) in several members of the mint family (Lamiaceae). The present study reports on the biochemical characterization of all Fd and FNR isoforms of peppermint (Mentha × piperita L.). The redox potentials of Fd and FNR isoforms were determined using photoreduction methods. Based on a diaphorase assay, peppermint R-FNR had a substantially higher specificity constant (kcat/Km) for NADPH than L-FNR. Similar results were obtained with ferricyanide as an electron acceptor. When assayed for NADPH-cytochrome c reductase activity, the specificity constant with the Fd II and Fd III isoforms (when compared to Fd I) was slightly higher for L-FNR and substantially higher for R-FNR. Based on real-time quantitative PCR assays with samples representing various peppermint organs and cell types, the Fd II gene was expressed very highly in metabolically active GTs (but also present at lower levels in roots), whereas Fd III was expressed at low levels in both roots and GTs. Our data provide evidence that high transcript levels of Fd II, and not differences in the biochemical properties of the encoded enzyme when compared to those of Fd III, are likely to support the formation of copious amounts of monoterpene via the MEP pathway in peppermint GTs. This work has laid the foundation for follow-up studies to further investigate the roles of a unique R-FNR-Fd II pair in non-photosynthetic GTs of the Lamiaceae.
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Affiliation(s)
| | | | | | | | - B. Markus Lange
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-7411, USA; (J.T.P.); (I.L.); (K.E.B.); (N.S.)
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2
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Polito JT, Lange BM. Standard operating procedures for the comprehensive and reliable analysis of cannabis terpenes. Methods Enzymol 2023; 680:381-419. [PMID: 36710020 DOI: 10.1016/bs.mie.2022.07.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Terpenes are the primary determinants of cannabis flower aroma, and ongoing research tests their potential for impacting the overall experience. Frustratingly, despite the importance of terpenes in cannabis physiology and commercial uses, literature reports vary widely regarding the major constituents of volatile blends and the concentrations of individual terpenes. In this article, we provide detailed descriptions of complementary approaches that will allow researchers to determine the identity and quantity of cannabis terpenes unequivocally and reliably. These standard operating procedures will guide decisions about which method to employ to address specific analytical goals. We are including two application examples to illustrate the utility of different approaches for tackling the analysis of terpenes in cannabis flower samples.
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Affiliation(s)
- Joshua T Polito
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States
| | - B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States; Dewey Scientific LLC, Pullman, WA, United States.
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3
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Fleming H, Chamberlain Z, Zager JJ, Lange BM. Controlled environments for cannabis cultivation to support "omics" research studies and production. Methods Enzymol 2023; 680:353-380. [PMID: 36710019 DOI: 10.1016/bs.mie.2022.07.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The cannabis (Cannabis sativa L.) genome is highly heterozygous and, to retain genetic identity, clonal propagation of cultivars is very common. Establishing controlled environments, often involving multiple locations throughout a single grow, is critical for reliably generating materials to be used in research and production. In this article, we break down different periods of the grow cycle, such as cloning, hardening (optional), vegetative growth, flowering growth, and harvest, into individual steps. We are including images and videos for an in-depth coverage of methodological details. We are providing a list of equipment, supplies, reagents, and other resources to help with planning a grow experiment. Finally, we are discussing considerations for different aspects of controlled environments, including lighting, fertilizer regimes, and integrated pest management. With this article, it is our goal to empower researchers to reliably generate disease-free cannabis material suitable for genetic and biochemical studies that require full control of environmental factors.
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Affiliation(s)
| | | | | | - B Markus Lange
- Dewey Scientific LLC, Pullman, WA, United States; Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States.
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4
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Lange BM, Srividya N, Lange I, Parrish AN, Benzenberg LR, Pandelova I, Vining KJ, Wüst M. Biochemical basis for the formation of organ-specific volatile blends in mint. Front Plant Sci 2023; 14:1125065. [PMID: 37123862 PMCID: PMC10140540 DOI: 10.3389/fpls.2023.1125065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Above-ground material of members of the mint family is commercially distilled to extract essential oils, which are then formulated into a myriad of consumer products. Most of the research aimed at characterizing the processes involved in the formation of terpenoid oil constituents has focused on leaves. We now demonstrate, by investigating three mint species, peppermint (Mentha ˣ piperita L.), spearmint (Mentha spicata L.) and horsemint (Mentha longifolia (L.) Huds.; accessions CMEN 585 and CMEN 584), that other organs - namely stems, rhizomes and roots - also emit volatiles and that the terpenoid volatile composition of these organs can vary substantially from that of leaves, supporting the notion that substantial, currently underappreciated, chemical diversity exists. Differences in volatile quantities released by plants whose roots had been dipped in a Verticillium dahliae-spore suspension (experimental) or dipped in water (controls) were evident: increases of some volatiles in the root headspace of mint species that are susceptible to Verticillium wilt disease (peppermint and M. longifolia CMEN 584) were detected, while the quantities of certain volatiles decreased in rhizomes of species that show resistance to the disease (spearmint and M. longifolia CMEN 585). To address the genetic and biochemical basis underlying chemical diversity, we took advantage of the newly sequenced M. longifolia CMEN 585 genome to identify candidate genes putatively coding for monoterpene synthases (MTSs), the enzymes that catalyze the first committed step in the biosynthesis of monoterpenoid volatiles. The functions of these genes were established by heterologous expression in Escherichia coli, purification of the corresponding recombinant proteins, and enzyme assays, thereby establishing the existence of MTSs with activities to convert a common substrate, geranyl diphosphate, to (+)-α-terpineol, 1,8-cineole, γ-terpinene, and (-)-bornyl diphosphate, but were not active with other potential substrates. In conjunction with previously described MTSs that catalyze the formation of (-)-β-pinene and (-)-limonene, the product profiles of the MTSs identified here can explain the generation of all major monoterpene skeletons represented in the volatiles released by different mint organs.
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Affiliation(s)
- B. Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, WashingtonState University, Pullman, WA, United States
- *Correspondence: B. Markus Lange,
| | - Narayanan Srividya
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, WashingtonState University, Pullman, WA, United States
| | - Iris Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, WashingtonState University, Pullman, WA, United States
| | - Amber N. Parrish
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, WashingtonState University, Pullman, WA, United States
| | - Lukas R. Benzenberg
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, WashingtonState University, Pullman, WA, United States
- Institut für Ernährungs- und Lebensmittelwissenschaften, Rheinische Friedrich Wilhelms-UniversitätBonn, Bonn, Germany
| | - Iovanna Pandelova
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Kelly J. Vining
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Matthias Wüst
- Institut für Ernährungs- und Lebensmittelwissenschaften, Rheinische Friedrich Wilhelms-UniversitätBonn, Bonn, Germany
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Paup VD, Barton TL, Edwards CG, Lange I, Lange BM, Lee J, Ross CF. Improving the chemical and sensory characteristics of red and white wines with pectinase‐producing non‐
Saccharomyces
yeasts. J Food Sci 2022; 87:5402-5417. [DOI: 10.1111/1750-3841.16371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 09/09/2022] [Accepted: 10/11/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Victoria D. Paup
- School of Food Science Washington State University Pullman Washington USA
| | - Tara L. Barton
- School of Food Science Washington State University Pullman Washington USA
| | - Charles G. Edwards
- School of Food Science Washington State University Pullman Washington USA
| | - Iris Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory Washington State University Pullman Washington USA
| | - B. Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory Washington State University Pullman Washington USA
| | - Jungmin Lee
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS) Horticultural Crops Research Unit Corvallis Oregon USA
| | - Carolyn F. Ross
- School of Food Science Washington State University Pullman Washington USA
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6
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Vining KJ, Pandelova I, Lange I, Parrish AN, Lefors A, Kronmiller B, Liachko I, Kronenberg Z, Srividya N, Lange BM. Chromosome-level genome assembly of Mentha longifolia L. reveals gene organization underlying disease resistance and essential oil traits. G3 Genes|Genomes|Genetics 2022; 12:6584825. [PMID: 35551385 PMCID: PMC9339296 DOI: 10.1093/g3journal/jkac112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 04/21/2022] [Indexed: 11/13/2022]
Abstract
Abstract
Mentha longifolia (L.) Huds., a wild, diploid mint species, has been developed as a model for mint genetic and genomic research to aid breeding efforts that target Verticillium wilt disease resistance and essential oil monoterpene composition. Here, we present a near-complete, chromosome-scale mint genome assembly for M. longifolia USDA accession CMEN 585. This new assembly is an update of a previously published genome draft, with dramatic improvements. A total of 42,107 protein-coding genes were annotated and placed on 12 chromosomal scaffolds. One hundred fifty-three genes contained conserved sequence domains consistent with nucleotide binding site-leucine-rich-repeat plant disease resistance genes. Homologs of genes implicated in Verticillium wilt resistance in other plant species were also identified. Multiple paralogs of genes putatively involved in p-menthane monoterpenoid biosynthesis were identified and several cases of gene clustering documented. Heterologous expression of candidate genes, purification of recombinant target proteins, and subsequent enzyme assays allowed us to identify the genes underlying the pathway that leads to the most abundant monoterpenoid volatiles. The bioinformatic and functional analyses presented here are laying the groundwork for using marker-assisted selection in improving disease resistance and essential oil traits in mints.
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Affiliation(s)
- Kelly J Vining
- Department of Horticulture, Oregon State University , Corvallis, OR 97331, USA
| | - Iovanna Pandelova
- Department of Horticulture, Oregon State University , Corvallis, OR 97331, USA
| | - Iris Lange
- M.J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University , Pullman, WA 99164-6340, USA
| | - Amber N Parrish
- M.J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University , Pullman, WA 99164-6340, USA
| | - Andrew Lefors
- M.J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University , Pullman, WA 99164-6340, USA
| | - Brent Kronmiller
- Center for Quantitative Life Sciences, Oregon State University , Corvallis, OR 97331, USA
| | | | | | - Narayanan Srividya
- M.J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University , Pullman, WA 99164-6340, USA
| | - B Markus Lange
- M.J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University , Pullman, WA 99164-6340, USA
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7
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Kim H, Srividya N, Lange I, Huchala EW, Ginovska B, Lange BM, Raugei S. Determinants of Selectivity for the Formation of Monocyclic and Bicyclic Products in Monoterpene Synthases. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hoshin Kim
- Physical and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Narayanan Srividya
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-7411, United States
| | - Iris Lange
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-7411, United States
| | - Eden W. Huchala
- Physical and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Bojana Ginovska
- Physical and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - B. Markus Lange
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-7411, United States
| | - Simone Raugei
- Physical and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-7411, United States
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8
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Liu C, Gao Q, Shang Z, Liu J, Zhou S, Dang J, Liu L, Lange I, Srividya N, Lange BM, Wu Q, Lin W. Corrigendum: Functional Characterization and Structural Insights Into Stereoselectivity of Pulegone Reductase in Menthol Biosynthesis. Front Plant Sci 2022; 12:828351. [PMID: 35095991 PMCID: PMC8796687 DOI: 10.3389/fpls.2021.828351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2021.780970.].
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Affiliation(s)
- Chanchan Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Qiyu Gao
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhuo Shang
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jian Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Siwei Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Beijing, China
| | - Jingjie Dang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Licheng Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Iris Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States
| | - Narayanan Srividya
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States
| | - B. Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States
| | - Qinan Wu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Wei Lin
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
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9
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Srividya N, Lange I, Richter JK, Wüst M, Lange BM. Selectivity of enzymes involved in the formation of opposite enantiomeric series of p-menthane monoterpenoids in peppermint and Japanese catnip. Plant Sci 2022; 314:111119. [PMID: 34895548 DOI: 10.1016/j.plantsci.2021.111119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/19/2021] [Accepted: 11/14/2021] [Indexed: 06/14/2023]
Abstract
Peppermint (Mentha x piperita L.) and Japanese catnip (Schizonepeta tenuifolia (Benth.) Briq.) accumulate p-menthane monoterpenoids with identical functionalization patterns but opposite stereochemistry. In the present study, we investigate the enantioselectivity of multiple enzymes involved in monoterpenoid biosynthesis in these species. Based on kinetic assays, mint limonene synthase, limonene 3-hydroxylase, isopiperitenol dehydrogenase, isopiperitenone reductase, and menthone reductase exhibited significant enantioselectivity toward intermediates of the pathway that proceeds through (-)-4S-limonene. Limonene synthase, isopiperitenol dehydrogenase and isopiperitenone reductase of Japanese catnip preferred intermediates of the pathway that involves (+)-4R-limonene, whereas limonene 3-hydroxylase was not enantioselective, and the activities of pulegone reductase and menthone reductase were too low to acquire meaningful kinetic data. Molecular modeling studies with docked ligands generally supported the experimental data obtained with peppermint enzymes, indicating that the preferred enantiomer was aligned well with the requisite cofactor and amino acid residues implicated in catalysis. A striking example for enantioselectivity was peppermint (-)-menthone reductase, which binds (-)-menthone with exquisite affinity but was predicted to bind (+)-menthone in a non-productive orientation that positions its carbonyl functional group at considerable distance to the NADPH cofactor. The work presented here lays the groundwork for structure-function studies aimed at unraveling how enantioselectivity evolved in closely related species of the Lamiaceae and beyond.
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Affiliation(s)
- Narayanan Srividya
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-7411, USA
| | - Iris Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-7411, USA
| | - Jana K Richter
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-7411, USA; Institut für Ernährungs- und Lebensmittelwissenschaften, Rheinische Friedrich-Wilhelms-Universität Bonn, Friedrich-Hirzebruch-Allee 7, 53115 Bonn, Germany
| | - Matthias Wüst
- Institut für Ernährungs- und Lebensmittelwissenschaften, Rheinische Friedrich-Wilhelms-Universität Bonn, Friedrich-Hirzebruch-Allee 7, 53115 Bonn, Germany
| | - B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-7411, USA.
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10
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Liu C, Gao Q, Shang Z, Liu J, Zhou S, Dang J, Liu L, Lange I, Srividya N, Lange BM, Wu Q, Lin W. Functional Characterization and Structural Insights Into Stereoselectivity of Pulegone Reductase in Menthol Biosynthesis. Front Plant Sci 2021; 12:780970. [PMID: 34917113 PMCID: PMC8670242 DOI: 10.3389/fpls.2021.780970] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/09/2021] [Indexed: 05/29/2023]
Abstract
Monoterpenoids are the main components of plant essential oils and the active components of some traditional Chinese medicinal herbs like Mentha haplocalyx Briq., Nepeta tenuifolia Briq., Perilla frutescens (L.) Britt and Pogostemin cablin (Blanco) Benth. Pulegone reductase is the key enzyme in the biosynthesis of menthol and is required for the stereoselective reduction of the Δ2,8 double bond of pulegone to produce the major intermediate menthone, thus determining the stereochemistry of menthol. However, the structural basis and mechanism underlying the stereoselectivity of pulegone reductase remain poorly understood. In this study, we characterized a novel (-)-pulegone reductase from Nepeta tenuifolia (NtPR), which can catalyze (-)-pulegone to (+)-menthone and (-)-isomenthone through our RNA-seq, bioinformatic analysis in combination with in vitro enzyme activity assay, and determined the structure of (+)-pulegone reductase from M. piperita (MpPR) by using X-ray crystallography, molecular modeling and docking, site-directed mutagenesis, molecular dynamics simulations, and biochemical analysis. We identified and validated the critical residues in the crystal structure of MpPR involved in the binding of the substrate pulegone. We also further identified that residues Leu56, Val282, and Val284 determine the stereoselectivity of the substrate pulegone, and mainly contributes to the product stereoselectivity. This work not only provides a starting point for the understanding of stereoselectivity of pulegone reductases, but also offers a basis for the engineering of menthone/menthol biosynthetic enzymes to achieve high-titer, industrial-scale production of enantiomerically pure products.
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Affiliation(s)
- Chanchan Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Qiyu Gao
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhuo Shang
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jian Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Siwei Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Beijing, China
| | - Jingjie Dang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Licheng Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Iris Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States
| | - Narayanan Srividya
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States
| | - B. Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States
| | - Qinan Wu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Wei Lin
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
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11
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Liu L, Yin M, Lin G, Wang Q, Zhou P, Dai S, Sang M, Lange BM, Liu C, Wu Q. Integrating RNA-seq with functional expression to analyze the regulation and characterization of genes involved in monoterpenoid biosynthesis in Nepeta tenuifolia Briq [Plant Physiol. Biochem. 167 (October 2021) 31-41]. Plant Physiol Biochem 2021; 167:911. [PMID: 34544008 DOI: 10.1016/j.plaphy.2021.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Affiliation(s)
- Licheng Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China
| | - Mengjiao Yin
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China
| | - Guyin Lin
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China
| | - Qian Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China
| | - Peina Zhou
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China
| | - Shilin Dai
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China
| | - Mengru Sang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China
| | - B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, 99164-7411, USA
| | - Chanchan Liu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China.
| | - Qinan Wu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, 210023, China.
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12
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Lange BM, Conner CF. Taxanes and taxoids of the genus Taxus - A comprehensive inventory of chemical diversity. Phytochemistry 2021; 190:112829. [PMID: 34329937 PMCID: PMC8393860 DOI: 10.1016/j.phytochem.2021.112829] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/12/2021] [Accepted: 06/02/2021] [Indexed: 05/05/2023]
Abstract
The pseudoalkaloid diterpene Taxol® (paclitaxel) emerged as a best-selling anti-cancer drug in the mid-1990s. The compound attracted considerable interest because of its unique mechanism to stabilize microtubules, thus reducing dynamicity and ultimately promoting mitotic arrest. Taxol was originally isolated from members of the genus Taxus. Over the last 50 years, close to 600 metabolites with taxane scaffolds were isolated from various Taxus species and their structures reported. The present review article provides an overview of the known chemical diversity of taxanes, with an emphasis on the functionalization of diterpene scaffolds. The implications of the occurrence of chemically diverse taxane metabolites for unraveling Taxol biosynthesis and enabling pathway engineering are discussed as well.
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Affiliation(s)
- B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, 99164-7411, USA.
| | - Caleb F Conner
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, 99164-7411, USA
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13
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Vining KJ, Hummer KE, Bassil NV, Lange BM, Khoury CK, Carver D. Crop Wild Relatives as Germplasm Resource for Cultivar Improvement in Mint ( Mentha L.). Front Plant Sci 2020; 11:1217. [PMID: 32973823 PMCID: PMC7466659 DOI: 10.3389/fpls.2020.01217] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 07/27/2020] [Indexed: 06/01/2023]
Abstract
Mentha is a strongly scented herb of the Lamiaceae (formerly Labiatae) and includes about 30 species and hybrid species that are distributed or introduced throughout the globe. These fragrant plants have been selected throughout millennia for use by humans as herbs, spices, and pharmaceutical needs. The distilling of essential oils from mint began in Japan and England but has become a significant industrial product for the US, China, India, and other countries. The US Department of Agriculture (USDA), Agricultural Research Service, National Clonal Germplasm Repository (NCGR) maintains a mint genebank in Corvallis, Oregon. This facility preserves and distributes about 450 clones representing 34 taxa, hybrid species, advanced breeder selections, and F1 hybrids. Mint crop wild relatives are included in this unique resource. The majority of mint accessions and hybrids in this collection were initially donated in the 1970s by the A.M. Todd Company, located in Kalamazoo, Michigan. Other representatives of diverse mint taxa and crop wild relatives have since been obtained from collaborators in Australia, New Zealand, Europe, and Vietnam. These mints have been evaluated for cytology, oil components, verticillium wilt resistance, and key morphological characters. Pressed voucher specimens have been prepared for morphological identity verification. An initial set of microsatellite markers has been developed to determine clonal identity and assess genetic diversity. Plant breeders at private and public institutions are using molecular analysis to determine identity and diversity of the USDA mint collection. Evaluation and characterization includes essential oil content, disease resistance, male sterility, and other traits for potential breeding use. These accessions can be a source for parental genes for enhancement efforts to produce hybrids, or for breeding new cultivars for agricultural production. Propagules of Mentha are available for distribution to international researchers as stem cuttings, rhizome cuttings, or seed, which can be requested through the GRIN-Global database of the US National Plant Germplasm System, subject to international treaty and quarantine regulations.
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Affiliation(s)
- Kelly J. Vining
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Kim E. Hummer
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
- National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR, United States
| | - Nahla V. Bassil
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
- National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR, United States
| | - B. Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States
| | - Colin K. Khoury
- Decision and Policy Analysis, International Center for Tropical Agriculture (CIAT), Cali, Colombia
- National Laboratory for Genetic Resources Preservation, Agricultural Research Service, United States Department of Agriculture, Fort Collins, CO, United States
| | - Dan Carver
- National Laboratory for Genetic Resources Preservation, Agricultural Research Service, United States Department of Agriculture, Fort Collins, CO, United States
- Colorado State University, Geospatial Centroid, Fort Collins, CO, United States
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14
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Lange I, Lange BM, Navarre DA. Altering potato isoprenoid metabolism increases biomass and induces early flowering. J Exp Bot 2020; 71:4109-4124. [PMID: 32296842 DOI: 10.1093/jxb/eraa185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
Isoprenoids constitute the largest class of plant natural products and have diverse biological functions including in plant growth and development. In potato (Solanum tuberosum), the regulatory mechanism underlying the biosynthesis of isoprenoids through the mevalonate pathway is unclear. We assessed the role of 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) homologs in potato development and in the metabolic regulation of isoprenoid biosynthesis by generating transgenic lines with down-regulated expression (RNAi-hmgr) or overexpression (OE) of one (StHMGR1 or StHMGR3) or two genes, HMGR and farnesyl diphosphate synthase (FPS; StHMGR1/StFPS1 or StHMGR3/StFPS1). Levels of sterols, steroidal glycoalkaloids (SGAs), and plastidial isoprenoids were elevated in the OE-HMGR1, OE-HMGR1/FPS1, and OE-HMGR3/FPS1 lines, and these plants exhibited early flowering, increased stem height, increased biomass, and increased total tuber weight. However, OE-HMGR3 lines showed dwarfism and had the highest sterol amounts, but without an increase in SGA levels, supporting a rate-limiting role for HMGR3 in the accumulation of sterols. Potato RNAi-hmgr lines showed inhibited growth and reduced cytosolic isoprenoid levels. We also determined the relative importance of transcriptional control at regulatory points of isoprenoid precursor biosynthesis by assessing gene-metabolite correlations. These findings provide novel insights into specific end-products of the sterol pathway and could be important for crop yield and bioenergy crops.
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Affiliation(s)
- Iris Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, USA
| | - B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, USA
| | - Duroy A Navarre
- Washington State University/IAREC, Prosser, WA, USA
- USDA/Agricultural Research Service, Prosser, WA, USA
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15
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Abstract
Monoterpene synthases catalyze the first committed step in the biosynthesis of monoterpenes and are in part responsible for the enormous structural diversity among this class of metabolites. Here, we explore the structure-function relationships underlying the formation of limonene enantiomers in limonene synthases that bind geranyl diphosphate as a common substrate. On the basis of analyses that consider both crystal structure data and amino acid sequence divergence, we identified candidate active site residues with potential roles in catalyzing reactions that involve accommodating reaction intermediates of opposite enantiomeric series. We demonstrate that spearmint (-)-limonene synthase [which generates >99% (-)-limonene over (+)-limonene] can be converted into a mutant enzyme, by exchanging four residues (C321S, N345I, I453V, and M458V), which produces (+)-limonene with reversed enantiospecificity [80% (+)-limonene and 3% (-)-limonene; the remainder are mostly bicyclic monoterpenes]. This study provides the foundation for a more in-depth understanding of the formation of enantiomeric series of monoterpenes, which can have vastly different olfactory properties.
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Affiliation(s)
- Narayanan Srividya
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340, United States
| | - Iris Lange
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340, United States
| | - B Markus Lange
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340, United States
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16
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Ahkami AH, Wang W, Wietsma TW, Winkler T, Lange I, Jansson C, Lange BM, McDowell NG. Metabolic shifts associated with drought-induced senescence in Brachypodium. Plant Sci 2019; 289:110278. [PMID: 31623774 DOI: 10.1016/j.plantsci.2019.110278] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 09/05/2019] [Accepted: 09/15/2019] [Indexed: 05/13/2023]
Abstract
The metabolic underpinnings of plant survival under severe drought-induced senescence conditions are poorly understood. In this study, we assessed the morphological, physiological and metabolic responses to sustained water deficit in Brachypodium distachyon, a model organism for research on temperate grasses. Relative to control plants, fresh biomass, leaf water potential, and chlorophyll levels decreased rapidly in plants grown under drought conditions, demonstrating an early onset of senescence. The leaf C/N ratio and protein content showed an increase in plants subjected to drought stress. The concentrations of several small molecule carbohydrates and amino acid-derived metabolites previously implicated in osmotic protection increased rapidly in plants experiencing water deficit. Malic acid, a low molecular weight organic acid with demonstrated roles in stomatal closure, also increased rapidly as a response to drought treatment. The concentrations of prenyl lipids, such as phytol and α-tocopherol, increased early during the drought treatment but then dropped dramatically. Surprisingly, continued changes in the quantities of metabolites were observed, even in samples harvested from visibly senesced plants. The data presented here provide insights into the processes underlying persistent metabolic activity during sustained water deficit and can aid in identifying mechanisms of drought tolerance in plants.
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Affiliation(s)
- Amir H Ahkami
- The Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, USA.
| | - Wenzhi Wang
- Earth Systems Science Division, Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | - Thomas W Wietsma
- The Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | - Tanya Winkler
- The Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | - Iris Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, USA
| | - Christer Jansson
- The Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, USA
| | - B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, USA
| | - Nate G McDowell
- Earth Systems Science Division, Pacific Northwest National Laboratory (PNNL), Richland, WA, USA.
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17
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Zager JJ, Lange I, Srividya N, Smith A, Lange BM. Gene Networks Underlying Cannabinoid and Terpenoid Accumulation in Cannabis. Plant Physiol 2019; 180:1877-1897. [PMID: 31138625 PMCID: PMC6670104 DOI: 10.1104/pp.18.01506] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 05/15/2019] [Indexed: 05/21/2023]
Abstract
Glandular trichomes are specialized anatomical structures that accumulate secretions with important biological roles in plant-environment interactions. These secretions also have commercial uses in the flavor, fragrance, and pharmaceutical industries. The capitate-stalked glandular trichomes of Cannabis sativa (cannabis), situated on the surfaces of the bracts of the female flowers, are the primary site for the biosynthesis and storage of resins rich in cannabinoids and terpenoids. In this study, we profiled nine commercial cannabis strains with purportedly different attributes, such as taste, color, smell, and genetic origin. Glandular trichomes were isolated from each of these strains, and cell type-specific transcriptome data sets were acquired. Cannabinoids and terpenoids were quantified in flower buds. Statistical analyses indicated that these data sets enable the high-resolution differentiation of strains by providing complementary information. Integrative analyses revealed a coexpression network of genes involved in the biosynthesis of both cannabinoids and terpenoids from imported precursors. Terpene synthase genes involved in the biosynthesis of the major monoterpenes and sesquiterpenes routinely assayed by cannabis testing laboratories were identified and functionally evaluated. In addition to cloning variants of previously characterized genes, specifically CsTPS14CT [(-)-limonene synthase] and CsTPS15CT (β-myrcene synthase), we functionally evaluated genes that encode enzymes with activities not previously described in cannabis, namely CsTPS18VF and CsTPS19BL (nerolidol/linalool synthases), CsTPS16CC (germacrene B synthase), and CsTPS20CT (hedycaryol synthase). This study lays the groundwork for developing a better understanding of the complex chemistry and biochemistry underlying resin accumulation across commercial cannabis strains.
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Affiliation(s)
- Jordan J Zager
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Iris Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Narayanan Srividya
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | | | - B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
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18
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Turner GW, Parrish AN, Zager JJ, Fischedick JT, Lange BM. Assessment of flux through oleoresin biosynthesis in epithelial cells of loblolly pine resin ducts. J Exp Bot 2019; 70:217-230. [PMID: 30312429 PMCID: PMC6305192 DOI: 10.1093/jxb/ery338] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 09/12/2018] [Indexed: 05/25/2023]
Abstract
The shoot system of pines contains abundant resin ducts, which harbor oleoresins that play important roles in constitutive and inducible defenses. In a pilot study, we assessed the chemical diversity of oleoresins obtained from mature tissues of loblolly pine trees (Pinus taeda L.). Building on these data sets, we designed experiments to assess oleoresin biosynthesis in needles of 2-year-old saplings. Comparative transcriptome analyses of single cell types indicated that genes involved in the biosynthesis of oleoresins are significantly enriched in isolated epithelial cells of resin ducts, compared with those expressed in mesophyll cells. Simulations using newly developed genome-scale models of epithelial and mesophyll cells, which incorporate our data on oleoresin yield and composition as well as gene expression patterns, predicted that heterotrophic metabolism in epithelial cells involves enhanced levels of oxidative phosphorylation and fermentation (providing redox and energy equivalents). Furthermore, flux was predicted to be more evenly distributed across the metabolic network of mesophyll cells, which, in contrast to epithelial cells, do not synthesize high levels of specialized metabolites. Our findings provide novel insights into the remarkable specialization of metabolism in epithelial cells.
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Affiliation(s)
- Glenn W Turner
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, USA
| | - Amber N Parrish
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, USA
| | - Jordan J Zager
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, USA
| | - Justin T Fischedick
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, USA
- Pure Analytics, Santa Rosa, CA, USA
| | - B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, USA
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19
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Šamec D, Pierz V, Srividya N, Wüst M, Lange BM. Assessing Chemical Diversity in Psilotum nudum (L.) Beauv., a Pantropical Whisk Fern That Has Lost Many of Its Fern-Like Characters. Front Plant Sci 2019; 10:868. [PMID: 31354756 PMCID: PMC6629931 DOI: 10.3389/fpls.2019.00868] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/18/2019] [Indexed: 05/10/2023]
Abstract
Members of the Psilotales (whisk ferns) have a unique anatomy, with conducting tissues but lacking true leaves and roots. Based on recent phyogenies, these features appear to represent a reduction from a more typical modern fern plant rather than the persistence of ancestral features. In this study, extracts of several Psilotum organs and tissues were analyzed by Gas Chromatography - Mass Spectrometry (GC-MS) and High Performance Liquid Chromatography - Quadrupole Time of Flight - Mass Spectrometry (HPLC-QTOF-MS). Some arylpyrones and biflavonoids had previously been reported to occur in Psilotum and these metabolite classes were found to be prominent constituents in the present study. Some of these were enriched and further characterized by Nuclear Magnetic Resonance (NMR) spectroscopy. HPLC-QTOF-MS and NMR data were searched against an updated Spektraris database (expanded by incorporating over 300 new arylpyrone and biflavonoid spectral records) to aid significantly with peak annotation. Principal Component Analysis (PCA) with combined GC-MS and HPLC-QTOF-MS data sets obtained with several Psilotum organs and tissues indicated a clear separation of the sample types. The principal component scores for below-ground rhizome samples corresponded to the vectors for carbohydrate monomers and dimers and small organic acids. Above-ground rhizome samples had principal component scores closer to the direction of vectors for arylpyrone glycosides and sucrose (which had high concentrations in above-and below-ground rhizomes). The unique position of brown synangia in a PCA plot correlated with the vector for biflavonoid glycosides. Principal component scores for green and yellow synangia correlated with the direction of vectors for arylpyrone glycosides and biflavonoid aglycones. Localization studies with cross sections of above-ground rhizomes, using Matrix-Assisted Laser Desorption/Ionization - Mass Spectrometry (MALDI-MS), provided evidence for a preferential accumulation of arylpyrone glycosides and biflavonoid aglycones in cells of the chlorenchyma. Our results indicate a differential localization of metabolites with potentially tissue-specific functions in defenses against biotic and abiotic stresses. The data are also a foundation for follow-up work to better understand chemical diversity in the Psilotales and other members of the fern lineage.
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Affiliation(s)
- Dunja Šamec
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States
- Ruđer Bošković Institute, Zagreb, Croatia
| | - Verena Pierz
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States
- Chair of Bioanalytics, Institute of Nutritional and Food Sciences, University of Bonn, Bonn, Germany
| | - Narayanan Srividya
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States
| | - Matthias Wüst
- Chair of Bioanalytics, Institute of Nutritional and Food Sciences, University of Bonn, Bonn, Germany
| | - B. Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, United States
- *Correspondence: B. Markus Lange,
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20
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Zager JJ, Lange BM. Assessing Flux Distribution Associated with Metabolic Specialization of Glandular Trichomes. Trends Plant Sci 2018; 23:638-647. [PMID: 29735428 DOI: 10.1016/j.tplants.2018.04.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/27/2018] [Accepted: 04/07/2018] [Indexed: 05/22/2023]
Abstract
Many aromatic plants accumulate mixtures of secondary (or specialized) metabolites in anatomical structures called glandular trichomes (GTs). Different GT types may also synthesize different mixtures of secreted metabolites, and this contributes to the enormous chemical diversity reported to occur across species. Over the past two decades, significant progress has been made in characterizing the genes and enzymes that are responsible for the unique metabolic capabilities of GTs in different lineages of flowering plants. Less is known about the processes that regulate flux distribution through precursor pathways toward metabolic end-products. We discuss here the results from a meta-analysis of genome-scale models that were developed to capture the unique metabolic capabilities of different GT types.
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Affiliation(s)
- Jordan J Zager
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164, USA
| | - B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164, USA.
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21
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Liu C, Srividya N, Parrish AN, Yue W, Shan M, Wu Q, Lange BM. Morphology of glandular trichomes of Japanese catnip (Schizonepeta tenuifolia Briquet) and developmental dynamics of their secretory activity. Phytochemistry 2018; 150:23-30. [PMID: 29533838 DOI: 10.1016/j.phytochem.2018.02.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 02/26/2018] [Accepted: 02/28/2018] [Indexed: 05/28/2023]
Abstract
Schizonepeta tenuifolia Briquet, commonly known as Japanese catnip, is used for the treatment of colds, headaches, fevers, and skin rashes in traditional Asian medicine (China, Japan and Korea). The volatile oil and its constituents have various demonstrated biological activities, but there is currently limited information regarding the site of biosynthesis. Light microscopy and scanning electron microscopy indicated the presence of three distinct glandular trichome types which, based on their morphological features, are referred to as peltate, capitate and digitiform glandular trichomes. Laser scanning microscopy and 3D reconstruction demonstrated that terpenoid-producing peltate glandular trichomes contain a disk of twelve secretory cells. The oil of peltate glandular trichomes, collected by laser microdissection or using custom-made micropipettes, was demonstrated to contain (-)-pulegone, (+)-menthone and (+)-limonene as major constituents. Digitiform and capitate glandular trichomes did not contain appreciable levels of terpenoid volatiles. The yield of distilled oil from spikes was significantly (44%) higher than that from leaves, while the composition of oils was very similar. Oils collected directly from leaf peltate glandular trichomes over the course of a growing season contained primarily (-)-pulegone (>80% at 32 days after germination) in young plants, while (+)-menthone began to accumulate later (>75% at 80 days after germination), at the expense of (-)-pulegone (the levels of (+)-limonene remained fairly stable at 3-5%). The current study establishes the morphological and chemical characteristics of glandular trichome types of S. tenuifolia, and also provides the basis for unraveling the biosynthesis of essential oil in this popular medicinal plant.
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Affiliation(s)
- Chanchan Liu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China; Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Narayanan Srividya
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Amber N Parrish
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Wei Yue
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Mingqiu Shan
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qinan Wu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA.
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22
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Vincelli P, Jackson-Smith D, Holsapple M, Grusak MA, Harsh M, Klein T, Lambert J, Lange BM, Lodge DM, McCluskey J, Murphy A, Neuhouser ML, Pray C, Weller S. National Academies report has broad support. Nat Biotechnol 2018; 35:304-306. [PMID: 28398324 DOI: 10.1038/nbt.3842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Paul Vincelli
- Sustainable Agriculture Research and Education Program (SARE) and the University of Kentucky, Lexington, Kentucky, USA
| | - Douglas Jackson-Smith
- Rural Sociological Society and School of Environment and Natural Resources, The Ohio State University, Columbus, Ohio, USA
| | - Michael Holsapple
- Society of Toxicology, Center for Research on Ingredient Safety (CRIS) and Department of Food Science and Human Nutrition, Michigan State University, East Lansing, Michigan, USA
| | - Michael A Grusak
- Crop Science Society of America, USDA-ARS Children's Nutrition Research Center and Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Matthew Harsh
- Society for Social Studies of Science and Centre for Engineering in Society, Concordia University, Montreal, Quebec, Canada
| | - Theodore Klein
- Society for In Vitro Biology and Meristematic, Inc., San Francisco, California, USA
| | - James Lambert
- Society for Risk Analysis and University of Virginia, Charlottesville, Virginia, USA
| | - B Markus Lange
- Phytochemical Society of North America and Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - David M Lodge
- Ecological Society of America and Atkinson Center for a Sustainable Future, Cornell University, Ithaca, New York, USA
| | - Jill McCluskey
- School of Economic Sciences, Washington State University, Pullman, Washington, USA
| | - Angus Murphy
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, Maryland, USA
| | - Marian L Neuhouser
- American Society for Nutrition and Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Carl Pray
- International Consortium for Applied Bioeconomy Research and Department of Agriculture, Food, and Resource Economics, Rutgers University, New Brunswick, New Jersey, USA
| | - Susan Weller
- Entomological Society of America and University of Nebraska State Museum, Lincoln, Nebraska, USA
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23
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Johnson SR, Lange I, Srividya N, Lange BM. Bioenergetics of Monoterpenoid Essential Oil Biosynthesis in Nonphotosynthetic Glandular Trichomes. Plant Physiol 2017; 175:681-695. [PMID: 28838953 PMCID: PMC5619891 DOI: 10.1104/pp.17.00551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/22/2017] [Indexed: 05/10/2023]
Abstract
The commercially important essential oils of peppermint (Mentha × piperita) and its relatives in the mint family (Lamiaceae) are accumulated in specialized anatomical structures called glandular trichomes (GTs). A genome-scale stoichiometric model of secretory phase metabolism in peppermint GTs was constructed based on current biochemical and physiological knowledge. Fluxes through the network were predicted based on metabolomic and transcriptomic data. Using simulated reaction deletions, this model predicted that two processes, the regeneration of ATP and ferredoxin (in its reduced form), exert substantial control over flux toward monoterpenes. Follow-up biochemical assays with isolated GTs indicated that oxidative phosphorylation and ethanolic fermentation were active and that cooperation to provide ATP depended on the concentration of the carbon source. We also report that GTs with high flux toward monoterpenes express, at very high levels, genes coding for a unique pair of ferredoxin and ferredoxin-NADP+ reductase isoforms. This study provides, to our knowledge, the first evidence of how bioenergetic processes determine flux through monoterpene biosynthesis in GTs.
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Affiliation(s)
- Sean R Johnson
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Iris Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Narayanan Srividya
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
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Inabuy FS, Fischedick JT, Lange I, Hartmann M, Srividya N, Parrish AN, Xu M, Peters RJ, Lange BM. Biosynthesis of Diterpenoids in Tripterygium Adventitious Root Cultures. Plant Physiol 2017; 175:92-103. [PMID: 28751314 PMCID: PMC5580761 DOI: 10.1104/pp.17.00659] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/18/2017] [Indexed: 05/22/2023]
Abstract
Adventitious root cultures were developed from Tripterygium regelii, and growth conditions were optimized for the abundant production of diterpenoids, which can be collected directly from the medium. An analysis of publicly available transcriptome data sets collected with T. regelii roots and root cultures indicated the presence of a large gene family (with 20 members) for terpene synthases (TPSs). Nine candidate diterpene synthase genes were selected for follow-up functional evaluation, of which two belonged to the TPS-c, three to the TPS-e/f, and four to the TPS-b subfamilies. These genes were characterized by heterologous expression in a modular metabolic engineering system in Escherichia coli Members of the TPS-c subfamily were characterized as copalyl diphosphate (diterpene) synthases, and those belonging to the TPS-e/f subfamily catalyzed the formation of precursors of kaurane diterpenoids. The TPS-b subfamily encompassed genes coding for enzymes involved in abietane diterpenoid biosynthesis and others with activities as monoterpene synthases. The structural characterization of diterpenoids accumulating in the medium of T. regelii adventitious root cultures, facilitated by searching the Spektraris online spectral database, enabled us to formulate a biosynthetic pathway for the biosynthesis of triptolide, a diterpenoid with pharmaceutical potential. Considering the significant enrichment of diterpenoids in the culture medium, fast-growing adventitious root cultures may hold promise as a sustainable resource for the large-scale production of triptolide.
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Affiliation(s)
- Fainmarinat S Inabuy
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Justin T Fischedick
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Iris Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Michael Hartmann
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Narayanan Srividya
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Amber N Parrish
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
| | - Meimei Xu
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011-1079
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011-1079
| | - B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340
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Vining KJ, Johnson SR, Ahkami A, Lange I, Parrish AN, Trapp SC, Croteau RB, Straub SCK, Pandelova I, Lange BM. Draft Genome Sequence of Mentha longifolia and Development of Resources for Mint Cultivar Improvement. Mol Plant 2017; 10:323-339. [PMID: 27867107 DOI: 10.1016/j.molp.2016.10.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 10/28/2016] [Accepted: 10/29/2016] [Indexed: 05/08/2023]
Abstract
The genus Mentha encompasses mint species cultivated for their essential oils, which are formulated into a vast array of consumer products. Desirable oil characteristics and resistance to the fungal disease Verticillium wilt are top priorities for the mint industry. However, cultivated mints have complex polyploid genomes and are sterile. Breeding efforts, therefore, require the development of genomic resources for fertile mint species. Here, we present draft de novo genome and plastome assemblies for a wilt-resistant South African accession of Mentha longifolia (L.) Huds., a diploid species ancestral to cultivated peppermint and spearmint. The 353 Mb genome contains 35 597 predicted protein-coding genes, including 292 disease resistance gene homologs, and nine genes determining essential oil characteristics. A genetic linkage map ordered 1397 genome scaffolds on 12 pseudochromosomes. More than two million simple sequence repeats were identified, which will facilitate molecular marker development. The M. longifolia genome is a valuable resource for both metabolic engineering and molecular breeding. This is exemplified by employing the genome sequence to clone and functionally characterize the promoters in a peppermint cultivar, and demonstrating the utility of a glandular trichome-specific promoter to increase expression of a biosynthetic gene, thereby modulating essential oil composition.
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Affiliation(s)
- Kelly J Vining
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA.
| | - Sean R Johnson
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Amirhossein Ahkami
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Iris Lange
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Amber N Parrish
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Susan C Trapp
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Rodney B Croteau
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Shannon C K Straub
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY 14456, USA
| | - Iovanna Pandelova
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
| | - B Markus Lange
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA.
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Lange BM, Fischedick JT, Lange MF, Srividya N, Šamec D, Poirier BC. Integrative Approaches for the Identification and Localization of Specialized Metabolites in Tripterygium Roots. Plant Physiol 2017; 173:456-469. [PMID: 27864443 PMCID: PMC5210757 DOI: 10.1104/pp.15.01593] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/13/2016] [Indexed: 05/16/2023]
Abstract
Members of the genus Tripterygium are known to contain an astonishing diversity of specialized metabolites. The lack of authentic standards has been an impediment to the rapid identification of such metabolites in extracts. We employed an approach that involves the searching of multiple, complementary chromatographic and spectroscopic data sets against the Spektraris database to speed up the metabolite identification process. Mass spectrometry-based imaging indicated a differential localization of triterpenoids to the periderm and sesquiterpene alkaloids to the cortex layer of Tripterygium roots. We further provide evidence that triterpenoids are accumulated to high levels in cells that contain suberized cell walls, which might indicate a mechanism for storage. To our knowledge, our data provide first insights into the cell type specificity of metabolite accumulation in Tripterygium and set the stage for furthering our understanding of the biological implications of specialized metabolites in this genus.
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Affiliation(s)
- B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340 (B.M.L., J.T.F., N.S., D.Š., B.C.P.);
- Undergraduate Program in Biochemistry, University of Washington, Seattle, Washington 98195-7350 (M.F.L.); and
- Ruđer Bošković Institute, Department of Molecular Biology, HR-10002 Zagreb, Croatia (D.Š.)
| | - Justin T Fischedick
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340 (B.M.L., J.T.F., N.S., D.Š., B.C.P.)
- Undergraduate Program in Biochemistry, University of Washington, Seattle, Washington 98195-7350 (M.F.L.); and
- Ruđer Bošković Institute, Department of Molecular Biology, HR-10002 Zagreb, Croatia (D.Š.)
| | - Malte F Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340 (B.M.L., J.T.F., N.S., D.Š., B.C.P.)
- Undergraduate Program in Biochemistry, University of Washington, Seattle, Washington 98195-7350 (M.F.L.); and
- Ruđer Bošković Institute, Department of Molecular Biology, HR-10002 Zagreb, Croatia (D.Š.)
| | - Narayanan Srividya
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340 (B.M.L., J.T.F., N.S., D.Š., B.C.P.)
- Undergraduate Program in Biochemistry, University of Washington, Seattle, Washington 98195-7350 (M.F.L.); and
- Ruđer Bošković Institute, Department of Molecular Biology, HR-10002 Zagreb, Croatia (D.Š.)
| | - Dunja Šamec
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340 (B.M.L., J.T.F., N.S., D.Š., B.C.P.)
- Undergraduate Program in Biochemistry, University of Washington, Seattle, Washington 98195-7350 (M.F.L.); and
- Ruđer Bošković Institute, Department of Molecular Biology, HR-10002 Zagreb, Croatia (D.Š.)
| | - Brenton C Poirier
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164-6340 (B.M.L., J.T.F., N.S., D.Š., B.C.P.)
- Undergraduate Program in Biochemistry, University of Washington, Seattle, Washington 98195-7350 (M.F.L.); and
- Ruđer Bošković Institute, Department of Molecular Biology, HR-10002 Zagreb, Croatia (D.Š.)
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Feldman MJ, Poirier BC, Lange BM. Misexpression of the Niemann-Pick disease type C1 (NPC1)-like protein in Arabidopsis causes sphingolipid accumulation and reproductive defects. Planta 2015; 242:921-33. [PMID: 26007685 DOI: 10.1007/s00425-015-2322-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/04/2015] [Indexed: 05/25/2023]
Abstract
Misexpression of the AtNPC1 - 1 and AtNPC1 - 2 genes leads to altered sphingolipid metabolism, growth impairment, and male reproductive defects in a hemizygous Arabidopsis thaliana (L.) double-mutant population. Abolishing the expression of both gene copies has lethal effects. Niemann-Pick disease type C1 is a lysosomal storage disorder caused by mutations in the NPC1 gene. At the cellular level, the disorder is characterized by the accumulation of storage lipids and lipid trafficking defects. The Arabidopsis thaliana genome contains two genes (At1g42470 and At4g38350) with weak homology to mammalian NPC1. The corresponding proteins have 11 predicted membrane-spanning regions and contain a putative sterol-sensing domain. The At1g42470 protein is localized to the plasma membrane, while At4g38350 protein has a dual localization in the plasma and tonoplast membranes. A phenotypic analysis of T-DNA insertion mutants indicated that At1g42470 and At4g38350 (designated AtNPC1-1 and AtNPC1-2, respectively) have partially redundant functions and are essential for plant reproductive viability and development. Homozygous plants impaired in the expression of both genes were not recoverable. Plants of a hemizygous AtNPC1-1/atnpc1-1/atnpc1-2/atnpc1-2 population were severely dwarfed and exhibited male gametophytic defects. These gene disruptions did not have an effect on sterol concentrations; however, hemizygous AtNPC1-1/atnpc1-1/atnpc1-2/atnpc1-2 mutants had increased fatty acid amounts. Among these, fatty acid α-hydroxytetracosanoic acid (h24:0) occurs in plant sphingolipids. Follow-up analyses confirmed the accumulation of significantly increased levels of sphingolipids (assayed as hydrolyzed sphingoid base component) in the hemizygous double-mutant population. Certain effects of NPC1 misexpression may be common across divergent lineages of eukaryotes (sphingolipid accumulation), while other defects (sterol accumulation) may occur only in certain groups of eukaryotic organisms.
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Affiliation(s)
- Maximilian J Feldman
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
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Fischedick JT, Johnson SR, Ketchum REB, Croteau RB, Lange BM. NMR spectroscopic search module for Spektraris, an online resource for plant natural product identification--Taxane diterpenoids from Taxus × media cell suspension cultures as a case study. Phytochemistry 2015; 113:87-95. [PMID: 25534952 PMCID: PMC4441555 DOI: 10.1016/j.phytochem.2014.11.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 10/13/2014] [Accepted: 10/14/2014] [Indexed: 05/04/2023]
Abstract
Development and testing of Spektraris-NMR, an online spectral resource, is reported for the NMR-based structural identification of plant natural products (PNPs). Spektraris-NMR allows users to search with multiple spectra at once and returns a table with a list of hits arranged according to the goodness of fit between query data and database entries. For each hit, a link to a tabulated alignment of (1)H NMR and (13)C NMR spectroscopic peaks (query versus database entry) is provided. Furthermore, full spectroscopic records and experimental meta information about each database entry can be accessed online. To test the utility of Spektraris-NMR for PNP identification, the database was populated with NMR data (total of 466 spectra) for ∼ 250 taxanes, which are structurally complex diterpenoids (including the anticancer drug taxol) commonly found in the genus Taxus. NMR data generated with metabolites purified from Taxus cell suspension cultures were then used to search Spektraris-NMR, and enabled the identification of eight taxanes with high confidence. A ninth isolated metabolite could be assigned, based on spectral searches, to a taxane skeletal class, but no high confidence hit was produced. Using various spectroscopic methods, this metabolite was characterized as 2-deacetylbaccatin IV, a novel taxane. These results indicate that Spektraris-NMR is a valuable resource for rapid and reliable identification of known metabolites and has the potential to contribute to de-replication efforts in novel PNP discovery.
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Affiliation(s)
- Justin T Fischedick
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Sean R Johnson
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Raymond E B Ketchum
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Rodney B Croteau
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - B Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA.
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May B, Lange BM, Wüst M. Biosynthesis of sesquiterpenes in grape berry exocarp of Vitis vinifera L.: evidence for a transport of farnesyl diphosphate precursors from plastids to the cytosol. Phytochemistry 2013; 95:135-44. [PMID: 23954075 PMCID: PMC3838315 DOI: 10.1016/j.phytochem.2013.07.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/16/2013] [Accepted: 07/22/2013] [Indexed: 05/20/2023]
Abstract
The participation of the mevalonic acid (MVA) and 1-deoxy-d-xylulose 5-phosphate/2-C-methyl-d-erythritol-4-phosphate (DOXP/MEP) pathways in sesquiterpene biosynthesis of grape berries was investigated. There is an increasing interest in this class of terpenoids, since the oxygenated sesquiterpene rotundone was identified as the peppery aroma impact compound in Australian Shiraz wines. To investigate precursor supply pathway utilization, in vivo feeding experiments were performed with the deuterium labeled, pathway specific, precursors [5,5-(2)H2]-1-deoxy-d-xylulose and [5,5-(2)H2]-mevalonic acid lactone. Head Space-Solid Phase Micro Extraction-Gas Chromatography-Mass Spectrometry (HS-SPME-GC-MS) analysis of the generated volatile metabolites demonstrated that de novo sesquiterpene biosynthesis is mainly located in the grape berry exocarp (skin), with no detectable activity in the mesocarp (flesh) of the Lemberger variety. Interestingly, precursors from both the (primarily) cytosolic MVA and plastidial DOXP/MEP pathways were incorporated into grape sesquiterpenes in the varieties Lemberger, Gewürztraminer and Syrah. Our labeling data provide evidence for a homogenous, cytosolic pool of precursors for sesquiterpene biosynthesis, indicating that a transport of precursors occurs mostly from plastids to the cytosol. The labeling patterns of the sesquiterpene germacrene D were in agreement with a cyclization mechanism analogous to that of a previously cloned enantioselective (R)-germacrene D synthase from Solidago canadensis. This observation was subsequently confirmed by enantioselective GC-MS analysis demonstrating the exclusive presence of (R)-germacrene D, and not the (S)-enantiomer, in grape berries.
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Affiliation(s)
- Bianca May
- University of Bonn, Department of Nutrition and Food Sciences, Bioanalytics, Endenicher Allee 11-13, D-53115 Bonn, Germany
| | - B. Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Matthias Wüst
- University of Bonn, Department of Nutrition and Food Sciences, Bioanalytics, Endenicher Allee 11-13, D-53115 Bonn, Germany
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Cuthbertson DJ, Johnson SR, Piljac-Žegarac J, Kappel J, Schäfer S, Wüst M, Ketchum REB, Croteau RB, Marques JV, Davin LB, Lewis NG, Rolf M, Kutchan TM, Soejarto DD, Lange BM. Accurate mass-time tag library for LC/MS-based metabolite profiling of medicinal plants. Phytochemistry 2013; 91:187-97. [PMID: 23597491 PMCID: PMC3697863 DOI: 10.1016/j.phytochem.2013.02.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 02/21/2013] [Accepted: 02/25/2013] [Indexed: 05/20/2023]
Abstract
We report the development and testing of an accurate mass-time (AMT) tag approach for the LC/MS-based identification of plant natural products (PNPs) in complex extracts. An AMT tag library was developed for approximately 500 PNPs with diverse chemical structures, detected in electrospray and atmospheric pressure chemical ionization modes (both positive and negative polarities). In addition, to enable peak annotations with high confidence, MS/MS spectra were acquired with three different fragmentation energies. The LC/MS and MS/MS data sets were integrated into online spectral search tools and repositories (Spektraris and MassBank), thus allowing users to interrogate their own data sets for the potential presence of PNPs. The utility of the AMT tag library approach is demonstrated by the detection and annotation of active principles in 27 different medicinal plant species with diverse chemical constituents.
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Affiliation(s)
- Daniel J. Cuthbertson
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Sean R. Johnson
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Jasenka Piljac-Žegarac
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
- Ruđer Bošković Institute, Bijenićka cesta 54, HR-10000 Zagreb, Croatia
| | - Julia Kappel
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
- Institute of Nutrition and Food Sciences, University of Bonn, Endenicher Allee 11-13, 53115 Bonn, Germany
| | - Sarah Schäfer
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
- Institute of Nutrition and Food Sciences, University of Bonn, Endenicher Allee 11-13, 53115 Bonn, Germany
| | - Matthias Wüst
- Institute of Nutrition and Food Sciences, University of Bonn, Endenicher Allee 11-13, 53115 Bonn, Germany
| | - Raymond E. B. Ketchum
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Rodney B. Croteau
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Joaquim V. Marques
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Laurence B. Davin
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Norman G. Lewis
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
| | - Megan Rolf
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
| | - Toni M. Kutchan
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
| | - D. Doel Soejarto
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St. (M/C 781), Chicago, IL 60612, USA
- Botany Department, Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605-2496, USA
| | - B. Markus Lange
- Institute of Biological Chemistry and M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA 99164-6340, USA
- Corresponding author: Tel.: 509-335-3794; fax: 509-335-7643. (B.M. Lange)
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Lange BM, Ahkami A. Metabolic engineering of plant monoterpenes, sesquiterpenes and diterpenes--current status and future opportunities. Plant Biotechnol J 2013; 11:169-96. [PMID: 23171352 DOI: 10.1111/pbi.12022] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 10/05/2012] [Accepted: 10/08/2012] [Indexed: 05/03/2023]
Abstract
Terpenoids (a.k.a. isoprenoids) represent the most diverse class of natural products found in plants, with tens of thousands of reported structures. Plant-derived terpenoids have a multitude of pharmaceutical and industrial applications, but the natural resources for their extraction are often limited and, in many cases, synthetic routes are not commercially viable. Some of the most valuable terpenoids are not accumulated in model plants or crops, and genetic resources for breeding of terpenoid natural product traits are thus poorly developed. At present, metabolic engineering, either in the native producer or a heterologous host, is the only realistic alternative to improve yield and accessibility. In this review article, we will evaluate the state of the art of modulating the biosynthetic pathways for the production of mono-, sesqui- and diterpenes in plants.
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Affiliation(s)
- B Markus Lange
- Institute of Biological Chemistry and MJ Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, USA.
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Lange BM, Turner GW. Terpenoid biosynthesis in trichomes--current status and future opportunities. Plant Biotechnol J 2013; 11:2-22. [PMID: 22979959 DOI: 10.1111/j.1467-7652.2012.00737.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 07/24/2012] [Accepted: 07/31/2012] [Indexed: 05/19/2023]
Abstract
Glandular trichomes are anatomical structures specialized for the synthesis of secreted natural products. In this review we focus on the description of glands that accumulate terpenoid essential oils and oleoresins. We also provide an in-depth account of the current knowledge about the biosynthesis of terpenoids and secretion mechanisms in the highly specialized secretory cells of glandular trichomes, and highlight the implications for metabolic engineering efforts.
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Affiliation(s)
- B Markus Lange
- Institute of Biological Chemistry, M.J. Murdock Metabolomics Laboratory, Washington State University, Pullman, WA, USA.
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Cuthbertson D, Andrews PK, Reganold JP, Davies NM, Lange BM. Utility of metabolomics toward assessing the metabolic basis of quality traits in apple fruit with an emphasis on antioxidants. J Agric Food Chem 2012; 60:8552-60. [PMID: 22881116 PMCID: PMC3551554 DOI: 10.1021/jf3031088] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A gas chromatography-mass spectrometry approach was employed to evaluate the use of metabolite patterns to differentiate fruit from six commercially grown apple cultivars harvested in 2008. Principal component analysis (PCA) of apple fruit peel and flesh data indicated that individual cultivar replicates clustered together and were separated from all other cultivar samples. An independent metabolomics investigation with fruit harvested in 2003 confirmed the separate clustering of fruit from different cultivars. Further evidence for cultivar separation was obtained using a hierarchical clustering analysis. An evaluation of PCA component loadings revealed specific metabolite classes that contributed the most to each principal component, whereas a correlation analysis demonstrated that specific metabolites correlate directly with quality traits such as antioxidant activity, total phenolics, and total anthocyanins, which are important parameters in the selection of breeding germplasm. These data sets lay the foundation for elucidating the metabolic basis of commercially important fruit quality traits.
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Affiliation(s)
- Daniel Cuthbertson
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, P.O. Box 646340, Pullman, Washington 99164-6340, United States
| | - Preston K. Andrews
- Department of Horticulture and Landscape Architecture, Washington State University, P.O. Box 646414, Pullman, Washington 99164-6414, United States
| | - John P. Reganold
- Department of Crop and Soil Sciences, Washington State University, P.O. Box 646420, Pullman, Washington 99164-6420, United States
| | - Neal M. Davies
- Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, P.O. Box 646510, Pullman, Washington 99164-6534, United States
| | - B. Markus Lange
- Institute of Biological Chemistry and M. J. Murdock Metabolomics Laboratory, Washington State University, P.O. Box 646340, Pullman, Washington 99164-6340, United States
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Voo SS, Grimes HD, Lange BM. Assessing the biosynthetic capabilities of secretory glands in Citrus peel. Plant Physiol 2012; 159:81-94. [PMID: 22452856 PMCID: PMC3375987 DOI: 10.1104/pp.112.194233] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 03/19/2012] [Indexed: 05/17/2023]
Abstract
Epithelial cells (ECs) lining the secretory cavities of Citrus peel have been hypothesized to be responsible for the synthesis of essential oil, but direct evidence for such a role is currently sparse. We used laser-capture microdissection and pressure catapulting to isolate ECs and parenchyma cells (as controls not synthesizing oil) from the peel of young grapefruit (Citrus × paradisi 'Duncan'), isolated RNA, and evaluated transcript patterns based on oligonucleotide microarrays. A Gene Ontology analysis of these data sets indicated an enrichment of genes involved in the biosynthesis of volatile terpenoids and nonvolatile phenylpropanoids in ECs (when compared with parenchyma cells), thus indicating a significant metabolic specialization in this cell type. The gene expression patterns in ECs were consistent with the accumulation of the major essential oil constituents (monoterpenes, prenylated coumarins, and polymethoxylated flavonoids). Morphometric analyses demonstrated that secretory cavities are formed early during fruit development, whereas the expansion of cavities, and thus oil accumulation, correlates with later stages of fruit expansion. Our studies have laid the methodological and experimental groundwork for a vastly improved knowledge of the as yet poorly understood processes controlling essential oil biosynthesis in Citrus peel.
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Affiliation(s)
- Siau Sie Voo
- Institute of Biological Chemistry (S.S.V., B.M.L.), M.J. Murdock Metabolomics Laboratory (B.M.L.), and School of Molecular Biosciences (H.D.G.), Washington State University, Pullman, Washington 99164–6340
| | - Howard D. Grimes
- Institute of Biological Chemistry (S.S.V., B.M.L.), M.J. Murdock Metabolomics Laboratory (B.M.L.), and School of Molecular Biosciences (H.D.G.), Washington State University, Pullman, Washington 99164–6340
| | - B. Markus Lange
- Institute of Biological Chemistry (S.S.V., B.M.L.), M.J. Murdock Metabolomics Laboratory (B.M.L.), and School of Molecular Biosciences (H.D.G.), Washington State University, Pullman, Washington 99164–6340
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Turner GW, Cuthbertson DJ, Voo SS, Settles ML, Grimes HD, Lange BM. Experimental sink removal induces stress responses, including shifts in amino acid and phenylpropanoid metabolism, in soybean leaves. Planta 2012; 235:939-54. [PMID: 22109846 PMCID: PMC3551543 DOI: 10.1007/s00425-011-1551-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 10/31/2011] [Indexed: 05/14/2023]
Abstract
The repeated removal of flower, fruit, or vegetative buds is a common treatment to simulate sink limitation. These experiments usually lead to the accumulation of specific proteins, which are degraded during later stages of seed development, and have thus been designated as vegetative storage proteins. We used oligonucleotide microarrays to assess global effects of sink removal on gene expression patterns in soybean leaves and found an induction of the transcript levels of hundreds of genes with putative roles in the responses to biotic and abiotic stresses. In addition, these data sets indicated potential changes in amino acid and phenylpropanoid metabolism. As a response to sink removal we detected an induced accumulation of γ-aminobutyric acid, while proteinogenic amino acid levels decreased. We also observed a shift in phenylpropanoid metabolism with an increase in isoflavone levels, concomitant with a decrease in flavones and flavonols. Taken together, we provide evidence that sink removal leads to an up-regulation of stress responses in distant leaves, which needs to be considered as an unintended consequence of this experimental treatment.
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Affiliation(s)
- Glenn W. Turner
- Institute of Biological Chemistry, M.J. Murdock Metabolomics Laboratory, Washington State University, P.O. Box 646340, Pullman, WA 99164-6340, USA
| | - Daniel J. Cuthbertson
- Institute of Biological Chemistry, M.J. Murdock Metabolomics Laboratory, Washington State University, P.O. Box 646340, Pullman, WA 99164-6340, USA
| | - Siau Sie Voo
- Institute of Biological Chemistry, M.J. Murdock Metabolomics Laboratory, Washington State University, P.O. Box 646340, Pullman, WA 99164-6340, USA
| | - Matthew L. Settles
- School of Molecular Biosciences (M.L.S., H.D.G.), Washington State University, P.O. Box 646340, Pullman, WA 99164-6340, USA
| | - Howard D. Grimes
- School of Molecular Biosciences (M.L.S., H.D.G.), Washington State University, P.O. Box 646340, Pullman, WA 99164-6340, USA
| | - B. Markus Lange
- Institute of Biological Chemistry, M.J. Murdock Metabolomics Laboratory, Washington State University, P.O. Box 646340, Pullman, WA 99164-6340, USA
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Quanbeck SM, Brachova L, Campbell AA, Guan X, Perera A, He K, Rhee SY, Bais P, Dickerson JA, Dixon P, Wohlgemuth G, Fiehn O, Barkan L, Lange I, Lange BM, Lee I, Cortes D, Salazar C, Shuman J, Shulaev V, Huhman DV, Sumner LW, Roth MR, Welti R, Ilarslan H, Wurtele ES, Nikolau BJ. Metabolomics as a Hypothesis-Generating Functional Genomics Tool for the Annotation of Arabidopsis thaliana Genes of "Unknown Function". Front Plant Sci 2012; 3:15. [PMID: 22645570 PMCID: PMC3355754 DOI: 10.3389/fpls.2012.00015] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 01/17/2012] [Indexed: 05/19/2023]
Abstract
Metabolomics is the methodology that identifies and measures global pools of small molecules (of less than about 1,000 Da) of a biological sample, which are collectively called the metabolome. Metabolomics can therefore reveal the metabolic outcome of a genetic or environmental perturbation of a metabolic regulatory network, and thus provide insights into the structure and regulation of that network. Because of the chemical complexity of the metabolome and limitations associated with individual analytical platforms for determining the metabolome, it is currently difficult to capture the complete metabolome of an organism or tissue, which is in contrast to genomics and transcriptomics. This paper describes the analysis of Arabidopsis metabolomics data sets acquired by a consortium that includes five analytical laboratories, bioinformaticists, and biostatisticians, which aims to develop and validate metabolomics as a hypothesis-generating functional genomics tool. The consortium is determining the metabolomes of Arabidopsis T-DNA mutant stocks, grown in standardized controlled environment optimized to minimize environmental impacts on the metabolomes. Metabolomics data were generated with seven analytical platforms, and the combined data is being provided to the research community to formulate initial hypotheses about genes of unknown function (GUFs). A public database (www.PlantMetabolomics.org) has been developed to provide the scientific community with access to the data along with tools to allow for its interactive analysis. Exemplary datasets are discussed to validate the approach, which illustrate how initial hypotheses can be generated from the consortium-produced metabolomics data, integrated with prior knowledge to provide a testable hypothesis concerning the functionality of GUFs.
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Affiliation(s)
- Stephanie M. Quanbeck
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
| | - Libuse Brachova
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
| | - Alexis A. Campbell
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
| | - Xin Guan
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
| | - Ann Perera
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
| | - Kun He
- Department of Plant Biology, Carnegie Institution for ScienceStanford, CA, USA
| | - Seung Y. Rhee
- Department of Plant Biology, Carnegie Institution for ScienceStanford, CA, USA
| | - Preeti Bais
- Bioinformatics and Computational Biology Program, Iowa State UniversityAmes, IA, USA
| | - Julie A. Dickerson
- Bioinformatics and Computational Biology Program, Iowa State UniversityAmes, IA, USA
| | - Philip Dixon
- Department of Statistics, Iowa State UniversityAmes, IA, USA
| | | | - Oliver Fiehn
- Genome Center, University of CaliforniaDavis, CA, USA
| | - Lenore Barkan
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State UniversityPullman, WA, USA
| | - Iris Lange
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State UniversityPullman, WA, USA
| | - B. Markus Lange
- M. J. Murdock Metabolomics Laboratory, Institute of Biological Chemistry, Washington State UniversityPullman, WA, USA
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei UniversitySeoul, Korea
| | - Diego Cortes
- Anatomy and Neurobiology, Virginia Commonwealth UniversityRichmond, VA, USA
| | - Carolina Salazar
- Department of Biological Sciences, University of North TexasDenton, TX, USA
| | - Joel Shuman
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
| | - Vladimir Shulaev
- Department of Biological Sciences, University of North TexasDenton, TX, USA
| | - David V. Huhman
- Plant Biology Division, The Samuel Roberts Noble FoundationArdmore, OK, USA
| | - Lloyd W. Sumner
- Plant Biology Division, The Samuel Roberts Noble FoundationArdmore, OK, USA
| | - Mary R. Roth
- Division of Biology, Kansas State UniversityManhattan, KS, USA
| | - Ruth Welti
- Division of Biology, Kansas State UniversityManhattan, KS, USA
| | - Hilal Ilarslan
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmes, IA, USA
| | - Eve S. Wurtele
- Department of Genetics, Development and Cell Biology, Iowa State UniversityAmes, IA, USA
| | - Basil J. Nikolau
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
- *Correspondence: Basil J. Nikolau, Iowa State University, 3254 Molecular Biology Building, Ames, IA 50011, USA. e-mail:
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Turner GW, Grimes HD, Lange BM. Soybean vegetative lipoxygenases are not vacuolar storage proteins. Funct Plant Biol 2011; 38:778-787. [PMID: 32480935 DOI: 10.1071/fp11047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 07/23/2011] [Indexed: 06/11/2023]
Abstract
The paraveinal mesophyll (PVM) of soybean is a distinctive uniseriate layer of branched cells situated between the spongy and palisade chlorenchyma of leaves that contains an abundance of putative vegetative storage proteins, Vspα and Vspβ, in its vacuoles. Soybean vegetative lipoxygenases (five isozymes designated as Vlx(A-E)) have been reported to co-localise with Vsp in PVM vacuoles; however, conflicting results regarding the tissue-level and subcellular localisations of specific Vlx isozymes have been reported. We employed immuno-cytochemistry with affinity-purified, isozyme-specific antibodies to reinvestigate the subcellular locations of soybean Vlx isozymes during a sink limitation experiment. VlxB and VlxC were localised to the cytoplasm and nucleoplasm of PVM cells, whereas VlxD was present in the cytoplasm and nucleoplasm of mesophyll chlorenchyma (MC) cells. Label was not associated with storage vacuoles or any evident protein bodies, so our results cast doubt on the hypothesis that Vlx isozymes function as vegetative storage proteins.
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Affiliation(s)
- Glenn W Turner
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
| | - Howard D Grimes
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - B Markus Lange
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA
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Bais P, Moon SM, He K, Leitao R, Dreher K, Walk T, Sucaet Y, Barkan L, Wohlgemuth G, Roth MR, Wurtele ES, Dixon P, Fiehn O, Lange BM, Shulaev V, Sumner LW, Welti R, Nikolau BJ, Rhee SY, Dickerson JA. PlantMetabolomics.org: a web portal for plant metabolomics experiments. Plant Physiol 2010; 152:1807-16. [PMID: 20147492 PMCID: PMC2850039 DOI: 10.1104/pp.109.151027] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 02/08/2010] [Indexed: 05/20/2023]
Abstract
PlantMetabolomics.org (PM) is a web portal and database for exploring, visualizing, and downloading plant metabolomics data. Widespread public access to well-annotated metabolomics datasets is essential for establishing metabolomics as a functional genomics tool. PM integrates metabolomics data generated from different analytical platforms from multiple laboratories along with the key visualization tools such as ratio and error plots. Visualization tools can quickly show how one condition compares to another and which analytical platforms show the largest changes. The database tries to capture a complete annotation of the experiment metadata along with the metabolite abundance databased on the evolving Metabolomics Standards Initiative. PM can be used as a platform for deriving hypotheses by enabling metabolomic comparisons between genetically unique Arabidopsis (Arabidopsis thaliana) populations subjected to different environmental conditions. Each metabolite is linked to relevant experimental data and information from various annotation databases. The portal also provides detailed protocols and tutorials on conducting plant metabolomics experiments to promote metabolomics in the community. PM currently houses Arabidopsis metabolomics data generated by a consortium of laboratories utilizing metabolomics to help elucidate the functions of uncharacterized genes. PM is publicly available at http://www.plantmetabolomics.org.
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Rios-Estepa R, Lange I, Lee JM, Lange BM. Mathematical modeling-guided evaluation of biochemical, developmental, environmental, and genotypic determinants of essential oil composition and yield in peppermint leaves. Plant Physiol 2010; 152:2105-19. [PMID: 20147490 PMCID: PMC2850044 DOI: 10.1104/pp.109.152256] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 02/04/2010] [Indexed: 05/04/2023]
Abstract
We have previously reported the use of a combination of computational simulations and targeted experiments to build a first generation mathematical model of peppermint (Menthaxpiperita) essential oil biosynthesis. Here, we report on the expansion of this approach to identify the key factors controlling monoterpenoid essential oil biosynthesis under adverse environmental conditions. We also investigated determinants of essential oil biosynthesis in transgenic peppermint lines with modulated essential oil profiles. A computational perturbation analysis, which was implemented to identify the variables that exert prominent control over the outputs of the model, indicated that the essential oil composition should be highly dependent on certain biosynthetic enzyme concentrations [(+)-pulegone reductase and (+)-menthofuran synthase], whereas oil yield should be particularly sensitive to the density and/or distribution of leaf glandular trichomes, the specialized anatomical structures responsible for the synthesis and storage of essential oils. A microscopic evaluation of leaf surfaces demonstrated that the final mature size of glandular trichomes was the same across all experiments. However, as predicted by the perturbation analysis, differences in the size distribution and the total number of glandular trichomes strongly correlated with differences in monoterpenoid essential oil yield. Building on various experimental data sets, appropriate mathematical functions were selected to approximate the dynamics of glandular trichome distribution/density and enzyme concentrations in our kinetic model. Based on a chi2 statistical analysis, simulated and measured essential oil profiles were in very good agreement, indicating that modeling is a valuable tool for guiding metabolic engineering efforts aimed at improving essential oil quality and quantity.
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Affiliation(s)
| | | | | | - B. Markus Lange
- Institute of Biological Chemistry (R.R.-E., I.L., B.M.L.), School of Chemical Engineering and Bioengineering (R.R.-E., J.M.L.), and M.J. Murdock Metabolomics Laboratory (B.M.L.), Washington State University, Pullman, Washington 99164–6340
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Ghassemian M, Lutes J, Chang HS, Lange I, Chen W, Zhu T, Wang X, Lange BM. Abscisic acid-induced modulation of metabolic and redox control pathways in Arabidopsis thaliana. Phytochemistry 2008; 69:2899-911. [PMID: 19007950 DOI: 10.1016/j.phytochem.2008.09.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2006] [Revised: 07/18/2008] [Accepted: 09/14/2008] [Indexed: 05/22/2023]
Abstract
Abscisic acid (ABA) has been implicated as a mediator in plant responses to various environmental stresses. To evaluate the transcriptional and metabolic events downstream of ABA perception, Arabidopsis thaliana seedlings were analyzed by transcript and metabolite profiling, and results were integrated, using the recently developed BioPathAt tool, in the context of the biochemical pathways affected by this treatment. Besides the up-regulation of pathways related to the biosynthesis of compatible solutes (raffinose family oligosaccharides and certain amino acids) as a response to ABA treatment, we also observed a down-regulation of numerous genes putatively localized to and possibly involved in the reorganization of cell walls, an association that had not been recognized previously. Metabolite profiling indicated that specific antioxidants, particularly alpha-tocopherol and L-ascorbic acid, were accumulated at higher levels in ABA-treated seedlings compared to appropriate controls. The transcription of genes involved in alpha-tocopherol biosynthesis were coordinately up-regulated and appeared to be integrated into a network of reactions controlling the levels of reactive oxygen species. Based upon the observed gene expression patterns, these redox control mechanisms might involve an ABA-mediated transition of mitochondrial respiration to the alternative, non-phosphorylating respiratory chain mode. The presented data herein provide indirect evidence for crosstalk between metabolic pathways and pathways regulating redox homeostasis as a response to ABA treatment, and allowed us to identify candidate genes for follow-up studies to dissect this interaction at the biochemical and molecular level. Our results also indicate an intricate relationship, at the transcriptional and possibly post-transcriptional levels, between ABA biosynthesis, the xanthophyll cycle, and ascorbic acid recycling.
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Cruz JA, Emery C, Wüst M, Kramer DM, Lange BM. Metabolite profiling of Calvin cycle intermediates by HPLC-MS using mixed-mode stationary phases. Plant J 2008; 55:1047-60. [PMID: 18494852 DOI: 10.1111/j.1365-313x.2008.03563.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
SUMMARY A sensitive and robust mixed-mode high performance liquid chromatography-tandem mass spectrometry method was developed for the qualitative and quantitative determination of sugar phosphates, which are notoriously difficult to separate using reversed-phase materials. Sugar phosphates were separated on a Primesep SB column by gradient elution using aqueous ammonium formate and acetonitrile as mobile phases. Target analytes were identified by their precursor/product ions and retention times. Quantitative analysis was performed in negative ionization/multiple reaction monitoring mode with five different time segments. The method was validated by spiking authentic sugar phosphate standards into complex plant tissue extracts. Standard curves of neat authentic standards and spiked extracts were generated for concentrations in the low picomole to nanomole range, with correlation coefficients of R(2) > 0.991, and the degree of ion suppression in the presence of a plant matrix was calculated for each analyte. Analyte recoveries, which were determined by including known quantities of authentic standards in the sugar phosphate extraction protocol, ranged from 40.0% to 57.4%. The analytical reproducibility was assessed by determining the coefficient of variance based on repeated extractions/measurements (<20%). The utility of our method is demonstrated with two types of applications: profiling of Calvin cycle intermediates in (i) dark-adapted and light-treated tobacco leaves, and in (ii) antisense plants expressing reduced levels of the Calvin cycle enzymes glyceraldehyde-3-phosphate dehydrogenase or ribulose-1,5-bisphosphate carboxylase/oxygenase (comparison with wild-type controls). The broader applicability of our method is illustrated by profiling sugar phosphates extracted from the leaves of five taxonomically diverse plants.
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Affiliation(s)
- Jeffrey A Cruz
- Institute of Biological Chemistry, Washington State University, Pullman, P.O. 646340, Washington 99164-6340, USA
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Mandaokar A, Thines B, Shin B, Lange BM, Choi G, Koo YJ, Yoo YJ, Choi YD, Choi G, Browse J. Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling. Plant J 2006; 46:984-1008. [PMID: 16805732 DOI: 10.1111/j.1365-313x.2006.02756.x] [Citation(s) in RCA: 225] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In Arabidopsis, jasmonate is required for stamen and pollen maturation. Mutants deficient in jasmonate synthesis, such as opr3, are male-sterile but become fertile when jasmonate is applied to developing flower buds. We have used ATH1 oligonucleotide arrays to follow gene expression in opr3 stamens for 22 h following jasmonate treatment. In these experiments, a total of 821 genes were specifically induced by jasmonate and 480 genes were repressed. Comparisons with data from previous studies indicate that these genes constitute a stamen-specific jasmonate transcriptome, with a large proportion (70%) of the genes expressed in the sporophytic tissue but not in the pollen. Bioinformatics tools allowed us to associate many of the induced genes with metabolic pathways that are probably upregulated during jasmonate-induced maturation. Our pathway analysis led to the identification of specific genes within larger families of homologues that apparently encode stamen-specific isozymes. Extensive additional analysis of our dataset identified 13 transcription factors that may be key regulators of the stamen maturation processes triggered by jasmonate. Two of these transcription factors, MYB21 and MYB24, are the only members of subgroup 19 of the R2R3 family of MYB proteins. A myb21 mutant obtained by reverse genetics exhibited shorter anther filaments, delayed anther dehiscence and greatly reduced male fertility. A myb24 mutant was phenotypically wild-type, but production of a myb21myb24 double mutant indicated that introduction of the myb24 mutation exacerbated all three aspects of the myb21 phenotype. Exogenous jasmonate could not restore fertility to myb21 or myb21myb24 mutant plants. Together with the data from transcriptional profiling, these results indicate that MYB21 and MYB24 are induced by jasmonate and mediate important aspects of the jasmonate response during stamen development.
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Affiliation(s)
- Ajin Mandaokar
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164-6340, USA
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Lange BM. Integrative analysis of metabolic networks: from peaks to flux models? Curr Opin Plant Biol 2006; 9:220-6. [PMID: 16581288 DOI: 10.1016/j.pbi.2006.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2006] [Accepted: 03/21/2006] [Indexed: 05/08/2023]
Abstract
Recent developments in genomic and post-genomic technologies have led to the amassment of data describing genome sequences, transcript, protein and metabolite abundances, protein modifications, and protein-protein and protein-DNA interactions. Such technologies have vastly expanded the inventory of detectable molecular species and can be used to describe their interdependence, but they have yet to fulfill their promise in enhancing our knowledge of how flux through metabolic pathways is regulated. A convergence of traditional reductionistic and novel holistic experimental approaches could aid in elucidating flux control.
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Affiliation(s)
- B Markus Lange
- Institute of Biological Chemistry and Center for Integrated Biotechnology, Washington State University, PO Box 646340, Pullman, WA 99164-6340, USA.
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Ghassemian M, Lutes J, Tepperman JM, Chang HS, Zhu T, Wang X, Quail PH, Lange BM. Integrative analysis of transcript and metabolite profiling data sets to evaluate the regulation of biochemical pathways during photomorphogenesis. Arch Biochem Biophys 2006; 448:45-59. [PMID: 16460663 DOI: 10.1016/j.abb.2005.11.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2005] [Revised: 10/24/2005] [Accepted: 11/01/2005] [Indexed: 10/25/2022]
Abstract
One of the key developmental processes during photomorphogenesis is the differentiation of prolamellar bodies of proplastids into thylakoid membranes containing the photosynthetic pigment-protein complexes of chloroplasts. To study the regulatory events controlling pigment-protein complex assembly, including the biosynthesis of metabolic precursors and pigment end products, etiolated Arabidopsis thaliana seedlings were irradiated with continuous red light (Rc), which led to rapid greening, or continuous far-red light (FRc), which did not result in visible greening, and subjected to analysis by oligonucleotide microarrays and targeted metabolite profiling. An analysis using BioPathAt, a bioinformatic tool that allows the visualization of post-genomic data sets directly on biochemical pathway maps, indicated that in Rc-treated seedlings mRNA expression and metabolite patterns were tightly correlated (e.g., Calvin cycle, biosynthesis of chlorophylls, carotenoids, isoprenoid quinones, thylakoid lipids, sterols, and amino acids). K-means clustering revealed that gene expression patterns across various biochemical pathways were very similar in Rc- and FRc-treated seedlings (despite the visible phenotypic differences), whereas a principal component analysis of metabolite pools allowed a clear distinction between both treatments (in accordance with the visible phenotype). Our results illustrate the general importance of integrative approaches to correlate post-genomic data sets with phenotypic outcomes.
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Affiliation(s)
- Majid Ghassemian
- Torrey Mesa Research Institute, 3115 Merryfield Row, San Diego, CA 92121, USA
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Abstract
The evolution of higher plants depended on the ability of cells to express hereditary information in many different ways and led to the development of specialized cell types, reflecting an elaborate system of control over gene expression in the individual component cells of various tissues. Bulk tissue sampling results in the loss of spatial resolution, and recent efforts have been directed toward improving access to specialized cell types in plants. Access to the contents of individual cells followed by analyses using post-genomic technologies promise to revolutionize our understanding of the differentiation of specialized cell types, and to enable downstream applications aimed at harnessing their unique biochemical properties.
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Affiliation(s)
- B Markus Lange
- Institute of Biological Chemistry and Center for Integrated Biotechnology, Washington State University, PO Box 646340, Pullman, Washington 99164-6340, USA.
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Jenkins H, Hardy N, Beckmann M, Draper J, Smith AR, Taylor J, Fiehn O, Goodacre R, Bino RJ, Hall R, Kopka J, Lane GA, Lange BM, Liu JR, Mendes P, Nikolau BJ, Oliver SG, Paton NW, Rhee S, Roessner-Tunali U, Saito K, Smedsgaard J, Sumner LW, Wang T, Walsh S, Wurtele ES, Kell DB. A proposed framework for the description of plant metabolomics experiments and their results. Nat Biotechnol 2005; 22:1601-6. [PMID: 15583675 DOI: 10.1038/nbt1041] [Citation(s) in RCA: 217] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The study of the metabolite complement of biological samples, known as metabolomics, is creating large amounts of data, and support for handling these data sets is required to facilitate meaningful analyses that will answer biological questions. We present a data model for plant metabolomics known as ArMet (architecture for metabolomics). It encompasses the entire experimental time line from experiment definition and description of biological source material, through sample growth and preparation to the results of chemical analysis. Such formal data descriptions, which specify the full experimental context, enable principled comparison of data sets, allow proper interpretation of experimental results, permit the repetition of experiments and provide a basis for the design of systems for data storage and transmission. The current design and example implementations are freely available (http://www.armet.org/). We seek to advance discussion and community adoption of a standard for metabolomics, which would promote principled collection, storage and transmission of experiment data.
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Affiliation(s)
- Helen Jenkins
- Department of Computer Science, University of Wales, Penglais, Aberystwyth, Ceredigion, Wales, UK
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Lange BM, Ghassemian M. Comprehensive post-genomic data analysis approaches integrating biochemical pathway maps. Phytochemistry 2005; 66:413-451. [PMID: 15694451 DOI: 10.1016/j.phytochem.2004.12.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2004] [Revised: 10/29/2004] [Indexed: 05/24/2023]
Abstract
Post-genomic era research is focusing on studies to attribute functions to genes and their encoded proteins, and to describe the regulatory networks controlling metabolic, protein synthesis and signal transduction pathways. To facilitate the analysis of experiments using post-genomic technologies, new concepts for linking the vast amount of raw data to a biological context have to be developed. Visual representations of pathways help biologists to understand the complex relationships between components of metabolic networks, and provide an invaluable resource for the integration of transcriptomics, proteomics and metabolomics data sets. Besides providing an overview of currently available bioinformatic tools for plant scientists, we introduce BioPathAt, a newly developed visual interface that allows the knowledge-based analysis of genome-scale data by integrating biochemical pathway maps (BioPathAtMAPS module) with a manually scrutinized gene-function database (BioPathAtDB) for the model plant Arabidopsis thaliana. In addition, we discuss approaches for generating a biochemical pathway knowledge database for A. thaliana that includes, in addition to accurate annotation, condensed experimental information regarding in vitro and in vivo gene/protein function.
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Affiliation(s)
- B Markus Lange
- Institute of Biological Chemistry and Center for Integrated Biotechnology, Washington State University, PO Box 646340, Pullman, WA 99164-6340, USA.
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Abstract
The centriole is a well-recognized, yet poorly understood, organelle present in many eukaryotic cells. Despite excellent electron-microscopic descriptions of its basic triplet microtubule structure, almost nothing is known of its specific molecular components. Here, Bodo Lange and Keith Gull survey centriole structure, duplication and maturation within the cell cycle and focus attention on the possible roles and function of centrioles as components of the centrosome in animal cells.
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Affiliation(s)
- B M Lange
- School of Biological Sciences, 2.205, Stopford Building, University of Manchester, Oxford Road, Manchester, UK M13 9PT.
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Affiliation(s)
- John Browse
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164-6340, USA.
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Bino RJ, Hall RD, Fiehn O, Kopka J, Saito K, Draper J, Nikolau BJ, Mendes P, Roessner-Tunali U, Beale MH, Trethewey RN, Lange BM, Wurtele ES, Sumner LW. Potential of metabolomics as a functional genomics tool. Trends Plant Sci 2004; 9:418-25. [PMID: 15337491 DOI: 10.1016/j.tplants.2004.07.004] [Citation(s) in RCA: 389] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- Raoul J Bino
- Plant Physiology Department, Wageningen University, Arboretumlaan 4, 6703 BD Wageningen, The Netherlands.
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